Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2102
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45528
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Found at i:2092 original size:27 final size:27
Alignment explanation
Indices: 2061--2237 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
2051 TAAATTGTAC
2061 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
2088 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2114 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
2142 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
2170 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
2197 AGCACTAAGTGTGCGAGTTGA-TATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2223 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2238 GACTCAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
26 17 0.13
27 88 0.69
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:2175 original size:82 final size:81
Alignment explanation
Indices: 2062--2217 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
2052 AAATTGTACA
* *
2062 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
2126 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
2143 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
2208 TGCGAGTTGA
65 TGCGAATTGA
2218 TATATAGCAC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:9940 original size:27 final size:27
Alignment explanation
Indices: 9909--10086 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
9899 TAAATTGTAC
*
9909 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
9936 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
9962 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
9990 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
10017 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
10045 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
10072 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
10087 GACTTAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:9970 original size:54 final size:55
Alignment explanation
Indices: 9909--10086 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 55
9899 TAAATTGTAC
* **
9909 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
9964 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* *
10017 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
*
10072 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
10087 GACTTAATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:15926 original size:48 final size:48
Alignment explanation
Indices: 15871--16100 Score: 217
Period size: 48 Copynumber: 4.9 Consensus size: 48
15861 AGGGTAAATT
* * * *
15871 GCCGATGCCATGTCCTAGACATGGTCTTACATTGGCTCTCATGTCGAG
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATATCAAG
* * * *
15919 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTTTCAAT
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATATCAAG
* * *
15967 GCCGATACCATGT-CT-G----GGTCTTACACTATCTCTCATAAT-ATG
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCAT-ATCAAG
* * *
16009 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCGT-ACATATCAAC
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGC-TCTCATATCAAG
* * *
16057 GCCGATGTCACGT-CTCAGACATGGTCTTACACTGGCTCTCATAT
1 GCCGATGCCATGTCCT-AGACATGGTCTTACACTAGCTCTCATAT
16101 TGTGGCTGAC
Statistics
Matches: 146, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
42 31 0.21
43 2 0.01
44 1 0.01
46 1 0.01
47 5 0.03
48 105 0.72
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (48 bp):
GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATATCAAG
Found at i:16127 original size:48 final size:48
Alignment explanation
Indices: 16075--16184 Score: 202
Period size: 48 Copynumber: 2.3 Consensus size: 48
16065 CACGTCTCAG
16075 ACATGGTCTTACACTGGCTCTCATATTGTGGCTGACACCATGTTGCAA
1 ACATGGTCTTACACTGGCTCTCATATTGTGGCTGACACCATGTTGCAA
* *
16123 ACATGGTCCTACATTGGCTCTCATATTGTGGCTGACACCATGTTGCAA
1 ACATGGTCTTACACTGGCTCTCATATTGTGGCTGACACCATGTTGCAA
16171 ACATGGTCTTACAC
1 ACATGGTCTTACAC
16185 ATAATAACGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (48 bp):
ACATGGTCTTACACTGGCTCTCATATTGTGGCTGACACCATGTTGCAA
Found at i:17416 original size:40 final size:40
Alignment explanation
Indices: 17372--17478 Score: 169
Period size: 40 Copynumber: 2.7 Consensus size: 40
17362 GTACATAGTC
*
17372 GAAGCTATCTCAAATCGCACACTAAGTGCCATATATAGCT
1 GAAGCTATGTCAAATCGCACACTAAGTGCCATATATAGCT
*
17412 GAAGCTATGTCAAATCACACACTAAGTGCCATATATAGCT
1 GAAGCTATGTCAAATCGCACACTAAGTGCCATATATAGCT
* **
17452 CAAGCTATGTCGTATCGCACACTAAGT
1 GAAGCTATGTCAAATCGCACACTAAGT
17479 TTCACAAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (40 bp):
GAAGCTATGTCAAATCGCACACTAAGTGCCATATATAGCT
Found at i:22949 original size:40 final size:40
Alignment explanation
Indices: 22837--22967 Score: 138
Period size: 40 Copynumber: 3.3 Consensus size: 40
22827 TTGATATCTT
* * * * *
22837 GCACACTAAGTGCCTTACATAGCTGAAGCTATCTCAAATC
1 GCACACTAAGTACCATATATAGCTGAAGCTATGTCGAATC
* * *
22877 GTACACTAAGTGCCATATACAG-TCGAAGCTATGTCGAATC
1 GCACACTAAGTACCATATATAGCT-GAAGCTATGTCGAATC
* * *
22917 ACACACTTAGTACCATATATAGCTGAAGCTATGTCGTATC
1 GCACACTAAGTACCATATATAGCTGAAGCTATGTCGAATC
*
22957 GCACATTAAGT
1 GCACACTAAGT
22968 GGCACAAATA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 1 0.01
40 72 0.97
41 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (40 bp):
GCACACTAAGTACCATATATAGCTGAAGCTATGTCGAATC
Found at i:29127 original size:28 final size:28
Alignment explanation
Indices: 29065--29137 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
29055 TATAAAGGTG
29065 AATTGGGCCTAGTGGGCCATAAGAATAT
1 AATTGGGCCTAGTGGGCCATAAGAATAT
* **
29093 AACTGGGCC-AGATGGGCCATTTGAATA-
1 AATTGGGCCTAG-TGGGCCATAAGAATAT
29120 AGATTGGGCCTAGTGGGC
1 A-ATTGGGCCTAGTGGGC
29138 TATATGCATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
27 3 0.08
28 33 0.87
29 2 0.05
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.23
Consensus pattern (28 bp):
AATTGGGCCTAGTGGGCCATAAGAATAT
Found at i:38565 original size:40 final size:39
Alignment explanation
Indices: 38474--38656 Score: 188
Period size: 40 Copynumber: 4.6 Consensus size: 39
38464 TCCTCGTTCA
* * **
38474 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTTTCAC
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
* *
38513 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
* *
38552 GAATGCCTTCGGGACTTAACCCGGATTTAGTACCTCGCAC
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
* * * * * *
38592 AAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCAC
*
38633 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
38657 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 36 0.30
40 77 0.64
41 8 0.07
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCAC
Found at i:38665 original size:41 final size:41
Alignment explanation
Indices: 38588--38665 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
38578 TTAGTACCTC
* * *
38588 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
38629 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
38666 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.